[Chimera-users] Placing markers in specific points of an EM map using command line

Tom Goddard goddard at sonic.net
Wed Aug 5 12:06:42 PDT 2015


When creating a movie usually I make a Chimera session file with all the models and markers, and I make a command script that carries out the action in the movie.  To record I open the session and then open the script.  It is much easier to set things up in a session then using commands.

To refer to an individual marker in a command you can use the residue number of the marker.  Each marker is in its own “residue”.

	display :5

  Tom


> On Aug 5, 2015, at 10:58 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Dear Ana-Lucia,
> There isn’t a command to do the same thing as manually creating and placing markers.  However, you already have the markers, so the work is done!  Just open the markers in Chimera and undisplay them before starting to record, and then only display them at the time you want them to be shown in your movie.  A marker set is implemented as a molecule model, and the markers as atoms, so you could just use “display” and “~display” commands to show and hide them, just like for atomic structures.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/display.html>
> 
> For example, if your marker set is open as model 3, the commands to hide and show the whole set could be: 
> ~disp #3
> disp #3
> To display them individually instead of a whole set at a time is tricker.  Normally I would use atom name or serial number, but the example marker file I’m using doesn’t have either of these assigned.  Maybe my coworkers can suggest how to specify the individual markers.
> 
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> On Aug 5, 2015, at 9:04 AM, Ana Lucia Alvarez Cabrera <anlualca at yahoo.com> wrote:
> 
>> Dear colleagues,
>> 
>> I would like to know how can I place markers in  specific points within an EM map, using commands (and not the Volume Tracer option in the graphic interface).
>> 
>> I am doing a movie and I need to place markers in different regions of a map. By placing the markers first manually with the mouse (using the Volume Tracer option in the graphic interface) into the map and saving the respective marker set I can know the specific coordinates for each marker by reading the output marker file "suffix.cmm" (for example: <marker id="1" x="22.28" y="24.608" z="17.976" r="1" g="0.49804" b="0" radius="2"/> ), but I still don't know how to use this information when writing the command for placing the marker in that position.
>> 
>> Thanks in advance,
>> 
>> Ana-Lucia
> 
> 
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